{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,7]],"date-time":"2024-08-07T17:51:17Z","timestamp":1723053077873},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1447,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,12,1]]},"abstract":"Abstract<\/jats:title>\n Motivation: Metagenomes are often characterized by high levels of unknown sequences. Reads derived from known microorganisms can easily be identified and analyzed using fast homology search algorithms and a suitable reference database, but the unknown sequences are often ignored in further analyses, biasing conclusions. Nevertheless, it is possible to use more data in a comparative metagenomic analysis by creating a cross-assembly of all reads, i.e. a single assembly of reads from different samples. Comparative metagenomics studies the interrelationships between metagenomes from different samples. Using an assembly algorithm is a fast and intuitive way to link (partially) homologous reads without requiring a database of reference sequences.<\/jats:p>\n Results: Here, we introduce crAss, a novel bioinformatic tool that enables fast simple analysis of cross-assembly files, yielding distances between all metagenomic sample pairs and an insightful image displaying the similarities.<\/jats:p>\n Availability and implementation: crAss is available as a web server at http:\/\/edwards.sdsu.edu\/crass\/, and the Perl source code can be downloaded to run as a stand-alone command line tool.<\/jats:p>\n Contact: \u00a0dutilh@cmbi.ru.nl<\/jats:p>\n Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts613","type":"journal-article","created":{"date-parts":[[2012,10,18]],"date-time":"2012-10-18T17:04:14Z","timestamp":1350579854000},"page":"3225-3231","source":"Crossref","is-referenced-by-count":58,"title":["Reference-independent comparative metagenomics using cross-assembly: crAss"],"prefix":"10.1093","volume":"28","author":[{"given":"Bas E.","family":"Dutilh","sequence":"first","affiliation":[{"name":"1 Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands, 2Department of Computer Science, 3Department of Biology, 4Computational Science Research Center and 5Department of Mathematics, San Diego State University, San Diego, CA 92182, USA and 6Division of Mathematics and Computer Science, Argonne National Laboratory, IL 60439, USA"},{"name":"1 Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands, 2Department of Computer Science, 3Department of Biology, 4Computational Science Research Center and 5Department of Mathematics, San Diego State University, San Diego, CA 92182, USA and 6Division of Mathematics and Computer Science, Argonne National Laboratory, IL 60439, USA"},{"name":"1 Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands, 2Department of Computer Science, 3Department of Biology, 4Computational Science Research Center and 5Department of Mathematics, San Diego State University, San Diego, CA 92182, USA and 6Division of Mathematics and Computer Science, Argonne National Laboratory, IL 60439, USA"}]},{"given":"Robert","family":"Schmieder","sequence":"additional","affiliation":[{"name":"1 Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands, 2Department of Computer Science, 3Department of Biology, 4Computational Science Research Center and 5Department of Mathematics, San Diego State University, San Diego, CA 92182, USA and 6Division of Mathematics and Computer Science, Argonne National Laboratory, IL 60439, USA"},{"name":"1 Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands, 2Department of Computer Science, 3Department of Biology, 4Computational Science Research Center and 5Department of Mathematics, San Diego State University, San Diego, CA 92182, USA and 6Division of Mathematics and Computer Science, Argonne National Laboratory, IL 60439, USA"}]},{"given":"Jim","family":"Nulton","sequence":"additional","affiliation":[{"name":"1 Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands, 2Department of Computer Science, 3Department of Biology, 4Computational Science Research Center and 5Department of Mathematics, San Diego State University, San Diego, CA 92182, USA and 6Division of Mathematics and Computer Science, Argonne National Laboratory, IL 60439, USA"}]},{"given":"Ben","family":"Felts","sequence":"additional","affiliation":[{"name":"1 Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands, 2Department of Computer Science, 3Department of Biology, 4Computational Science Research Center and 5Department of Mathematics, San Diego State University, San Diego, CA 92182, USA and 6Division of Mathematics and Computer Science, Argonne National Laboratory, IL 60439, USA"}]},{"given":"Peter","family":"Salamon","sequence":"additional","affiliation":[{"name":"1 Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands, 2Department of Computer Science, 3Department of Biology, 4Computational Science Research Center and 5Department of Mathematics, San Diego State University, San Diego, CA 92182, USA and 6Division of Mathematics and Computer Science, Argonne National Laboratory, IL 60439, USA"}]},{"given":"Robert A.","family":"Edwards","sequence":"additional","affiliation":[{"name":"1 Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands, 2Department of Computer Science, 3Department of Biology, 4Computational Science Research Center and 5Department of Mathematics, San Diego State University, San Diego, CA 92182, USA and 6Division of Mathematics and Computer Science, Argonne National Laboratory, IL 60439, USA"},{"name":"1 Centre for Molecular and Biomolecular 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